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Illumina / REViewer

A tool for visualizing alignments of reads in regions containing tandem repeats
GNU General Public License v3.0
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[error] No VCF record for C9ORF72 #54

Open mital14 opened 2 years ago

mital14 commented 2 years ago

image

I am getting this error! what could be the reason?

sclamons commented 2 years ago

Usually this happens to me when I don't use give REViewer the correct VCF output from a prior ExpansionHunter run, or if I accidentally switched variant catalogs between ExpansionHunter and REViewer.

It could also happen if there weren't any alignments to the C90RF72 gene. Have you verified that there is at least one sequence in your ExpansionHunter output that maps to C90RF72?

If it isn't one of those, can you post or send me your data, locus catalog, and VCF? I realize it might not be data you can share, but if it is, I can do more to help diagnose the error.

ghost commented 10 months ago

Hello. I'm getting the same error but for another locus. I used the variant catalog that I used for running ExpansionHunter, and the VCF that was generated by EH, and EH-sorted-indexed bam files. The VCF files has a record for the locus of interest. Are we supposed to generate a different variant catalog for REViewer or just use the one we used for running EH or use the one that was generated by EH?

sclamons commented 10 months ago

You should be able to use the locus catalogue that you used for EH. Can you send me an example bam, catalog file, locus file (and locus of interest), and which genome build you used?

On Mon, Dec 4, 2023, 3:08 PM Azjer2014 @.***> wrote:

Hello. I'm getting the same error but for another locus. I used the variant catalog that I used for running ExpansionHunter, and the VCF that was generated by EH, and EH-sorted-indexed bam files. The VCF files has a record for the locus of interest. Are we supposed to generate a different variant catalog for REViewer or just use the one we used for running EH or use the one that was generated by EH?

— Reply to this email directly, view it on GitHub https://github.com/Illumina/REViewer/issues/54#issuecomment-1839394857, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAM7DU5RSMFRTFKVAJXVBCTYHYUVVAVCNFSM53VJGN72U5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TCOBTHEZTSNBYGU3Q . You are receiving this because you commented.Message ID: @.***>

ghost commented 10 months ago

It turned out that the compressed VCF file was the issue. After decompressing it, everything worked fine. The error message was not informative.